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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SpatialFeatureExperiment_1.15.0.tar.gz','quit-with-status'=TRUE)"
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── Installing SpatialFeatureExperiment ─────────────────────────────────────────
✔ Package installed successfully
── SpatialFeatureExperiment session metadata ───────────────────────────────────
→ sourceDir: /tmp/RtmpByxgeW/file1449767835e912/SpatialFeatureExperiment
→ BiocVersion: 3.24
→ Package: SpatialFeatureExperiment
→ PackageVersion: 1.15.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SpatialFeatureExperiment.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpByxgeW/file1449767835e912/SpatialFeatureExperiment
→ installDir: /tmp/RtmpByxgeW/file144976485eb43f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SpatialFeatureExperiment ───────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
✖ ERROR: Package dependencies must be on CRAN or Bioconductor. Remove
'Remotes:' from DESCRIPTION
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.3.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: DataImport
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (40%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • SFE.Rmd
* Checking package installation calls in R code...
* Checking for library/require of SpatialFeatureExperiment...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/coerce.R (line 406, column 19)
    • R/coerce.R (line 634, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • coerce.R (line 241, column 41)
    • ...
    • transformation.R (line 193, column 28)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/coerce.R (line 312, column 23)
    • ...
    • R/read.R (line 872, column 25)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 12 times)
  • suppressWarnings() in R/coerce.R (line 46, column 17)
  • ...
  • suppressWarnings() in R/utils.R (line 295, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 29
functions greater than 50 lines.
  The longest 5 functions are:
    • .seu_to_sfe() (R/coerce.R): 471 lines
    • ...
    • .read10xVisium() (R/read.R): 192 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/colGeometries.Rd
    • ...
    • man/SFE-image.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • affineImg.Rd
    • ...
    • transposeImg.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 1% of man
pages use at least one of these tags.
  Found in files:
    • SpatialFeatureExperiment-subset.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
ℹ NOTE: skip_on_bioc() found in testthat files: test-read.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 502 lines (4%) are > 80 characters long.
  First few lines:
    • R/aggregate.R#L59 new_geometry_nam ...
    • ...
    • vignettes/SFE.Rmd#L606 6. Setting units of length in the SFE ob ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1416 lines (11%) are
not.
  First few lines:
    • R/aggregate.R#L68 min_phred, fl ...
    • ...
    • vignettes/SFE.Rmd#L536 annotGeome ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | ℹ 14 NOTES
ℹ See the SpatialFeatureExperiment.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.